data_2D7R # _model_server_result.job_id 6NSv1XIUanw_Png1IAGbGw _model_server_result.datetime_utc '2025-02-27 01:45:20' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 2d7r # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":707}' # _entry.id 2D7R # _exptl.entry_id 2D7R _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 2D7R _cell.length_a 80.195 _cell.length_b 132.812 _cell.length_c 138.953 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2D7R _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id G _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B NAG 1 B 1 NAG B 700 NAG 2 n B NAG 2 B 2 NAG B 703 NAG # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order disulf ? disulf1 A SG CYS 102 A CYS 135 1_555 A SG CYS 332 A CYS 365 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf2 A SG CYS 323 A CYS 356 1_555 A SG CYS 399 A CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf3 A SG CYS 438 A CYS 471 1_555 A SG CYS 455 A CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf4 A SG CYS 490 A CYS 523 1_555 A SG CYS 505 A CYS 538 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf5 A SG CYS 530 A CYS 563 1_555 A SG CYS 545 A CYS 578 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? covale ? covale1 A ND2 ASN 91 A ASN 124 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale2 A ND2 ASN 113 A ASN 146 1_555 E C1 NAG . A NAG 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale3 A ND2 ASN 560 A ASN 593 1_555 C C1 NAG . A NAG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale4 H OG SER . A SER 708 1_555 I C1 A2G . A A2G 709 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 sing covale ? covale5 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.395 ? metalc ? metalc1 A OD2 ASP 204 A ASP 237 1_555 F MN MN . A MN 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? metalc ? metalc2 A NE2 HIS 206 A HIS 239 1_555 F MN MN . A MN 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc3 A NE2 HIS 337 A HIS 370 1_555 F MN MN . A MN 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? metalc ? metalc4 F MN MN . A MN 706 1_555 G O1A UDP . A UDP 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc5 F MN MN . A MN 706 1_555 G O3B UDP . A UDP 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? metalc ? metalc6 F MN MN . A MN 706 1_555 J O HOH . A HOH 816 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? # _chem_comp.formula 'C9 H14 N2 O12 P2' _chem_comp.formula_weight 404.161 _chem_comp.id UDP _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag N1 C2 UDP sing 448 n n N1 C6 UDP sing 449 n n N1 C1' UDP sing 450 n n C2 N3 UDP sing 451 n n C2 O2 UDP doub 452 n n N3 C4 UDP sing 453 n n N3 HN3 UDP sing 454 n n C4 C5 UDP sing 455 n n C4 O4 UDP doub 456 n n C5 C6 UDP doub 457 n n C5 H5 UDP sing 458 n n C6 H6 UDP sing 459 n n C1' C2' UDP sing 460 n n C1' O4' UDP sing 461 n n C1' H1' UDP sing 462 n n C2' O2' UDP sing 463 n n C2' C3' UDP sing 464 n n C2' H2' UDP sing 465 n n O2' HO2' UDP sing 466 n n C3' C4' UDP sing 467 n n C3' O3' UDP sing 468 n n C3' H3' UDP sing 469 n n C4' O4' UDP sing 470 n n C4' C5' UDP sing 471 n n C4' H4' UDP sing 472 n n O3' HO3' UDP sing 473 n n C5' O5' UDP sing 474 n n C5' "H5'1" UDP sing 475 n n C5' "H5'2" UDP sing 476 n n O5' PA UDP sing 477 n n PA O1A UDP doub 478 n n PA O2A UDP sing 479 n n PA O3A UDP sing 480 n n O2A HOA2 UDP sing 481 n n O3A PB UDP sing 482 n n PB O1B UDP doub 483 n n PB O2B UDP sing 484 n n PB O3B UDP sing 485 n n O2B HOB2 UDP sing 486 n n O3B HOB3 UDP sing 487 n n # _atom_sites.entry_id 2D7R _atom_sites.fract_transf_matrix[1][1] 0.01247 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007529 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.007197 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code C 3 NAG A 1 703 701 NAG NAG . D 4 NGA A 1 704 702 NGA NGA . E 3 NAG A 1 705 704 NAG NAG . F 5 MN A 1 706 706 MN MN . G 6 UDP A 1 707 705 UDP UDP . H 7 SER A 1 708 707 SER TNR . I 8 A2G A 1 709 707 A2G TNR . J 9 HOH A 1 801 727 HOH HOH . J 9 HOH A 2 802 721 HOH HOH . J 9 HOH A 3 803 744 HOH HOH . J 9 HOH A 4 804 722 HOH HOH . J 9 HOH A 5 805 750 HOH HOH . J 9 HOH A 6 806 783 HOH HOH . J 9 HOH A 7 807 734 HOH HOH . J 9 HOH A 8 808 730 HOH HOH . J 9 HOH A 9 809 712 HOH HOH . J 9 HOH A 10 810 714 HOH HOH . J 9 HOH A 11 811 716 HOH HOH . J 9 HOH A 12 812 720 HOH HOH . J 9 HOH A 13 813 760 HOH HOH . J 9 HOH A 14 814 728 HOH HOH . J 9 HOH A 15 815 723 HOH HOH . J 9 HOH A 16 816 711 HOH HOH . J 9 HOH A 17 817 770 HOH HOH . J 9 HOH A 18 818 718 HOH HOH . J 9 HOH A 19 819 719 HOH HOH . J 9 HOH A 20 820 763 HOH HOH . J 9 HOH A 21 821 715 HOH HOH . J 9 HOH A 22 822 780 HOH HOH . J 9 HOH A 23 823 771 HOH HOH . J 9 HOH A 24 824 753 HOH HOH . J 9 HOH A 25 825 755 HOH HOH . J 9 HOH A 26 826 746 HOH HOH . J 9 HOH A 27 827 729 HOH HOH . J 9 HOH A 28 828 738 HOH HOH . J 9 HOH A 29 829 745 HOH HOH . J 9 HOH A 30 830 773 HOH HOH . J 9 HOH A 31 831 713 HOH HOH . J 9 HOH A 32 832 765 HOH HOH . J 9 HOH A 33 833 778 HOH HOH . J 9 HOH A 34 834 784 HOH HOH . J 9 HOH A 35 835 758 HOH HOH . J 9 HOH A 36 836 782 HOH HOH . J 9 HOH A 37 837 761 HOH HOH . J 9 HOH A 38 838 717 HOH HOH . J 9 HOH A 39 839 764 HOH HOH . J 9 HOH A 40 840 740 HOH HOH . J 9 HOH A 41 841 779 HOH HOH . J 9 HOH A 42 842 726 HOH HOH . J 9 HOH A 43 843 767 HOH HOH . J 9 HOH A 44 844 768 HOH HOH . J 9 HOH A 45 845 725 HOH HOH . J 9 HOH A 46 846 743 HOH HOH . J 9 HOH A 47 847 732 HOH HOH . J 9 HOH A 48 848 756 HOH HOH . J 9 HOH A 49 849 735 HOH HOH . J 9 HOH A 50 850 769 HOH HOH . J 9 HOH A 51 851 748 HOH HOH . J 9 HOH A 52 852 752 HOH HOH . J 9 HOH A 53 853 757 HOH HOH . J 9 HOH A 54 854 742 HOH HOH . J 9 HOH A 55 855 781 HOH HOH . J 9 HOH A 56 856 749 HOH HOH . J 9 HOH A 57 857 731 HOH HOH . J 9 HOH A 58 858 766 HOH HOH . J 9 HOH A 59 859 747 HOH HOH . J 9 HOH A 60 860 774 HOH HOH . J 9 HOH A 61 861 751 HOH HOH . J 9 HOH A 62 862 762 HOH HOH . J 9 HOH A 63 863 772 HOH HOH . J 9 HOH A 64 864 741 HOH HOH . J 9 HOH A 65 865 775 HOH HOH . J 9 HOH A 66 866 777 HOH HOH . J 9 HOH A 67 867 754 HOH HOH . J 9 HOH A 68 868 736 HOH HOH . J 9 HOH A 69 869 759 HOH HOH . J 9 HOH A 70 870 739 HOH HOH . J 9 HOH A 71 871 724 HOH HOH . J 9 HOH A 72 872 733 HOH HOH . J 9 HOH A 73 873 737 HOH HOH . J 9 HOH A 74 874 776 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 N N1 UDP . . . G 6 15.707 45.322 23.521 1 53.55 ? N1 UDP 707 A 1 HETATM 2 C C2 UDP . . . G 6 16.41 45.342 24.72 1 52.25 ? C2 UDP 707 A 1 HETATM 3 N N3 UDP . . . G 6 16.994 46.506 25.145 1 50.51 ? N3 UDP 707 A 1 HETATM 4 C C4 UDP . . . G 6 16.89 47.658 24.395 1 49.83 ? C4 UDP 707 A 1 HETATM 5 C C5 UDP . . . G 6 16.194 47.652 23.184 1 50.01 ? C5 UDP 707 A 1 HETATM 6 C C6 UDP . . . G 6 15.684 46.436 22.713 1 53.27 ? C6 UDP 707 A 1 HETATM 7 O O2 UDP . . . G 6 16.517 44.336 25.422 1 53.76 ? O2 UDP 707 A 1 HETATM 8 O O4 UDP . . . G 6 17.423 48.68 24.811 1 52.47 ? O4 UDP 707 A 1 HETATM 9 C C1' UDP . . . G 6 15.119 44.043 23.087 1 54.01 ? C1' UDP 707 A 1 HETATM 10 C C2' UDP . . . G 6 13.746 44.119 22.45 1 54.18 ? C2' UDP 707 A 1 HETATM 11 O O2' UDP . . . G 6 12.728 43.976 23.418 1 56.39 ? O2' UDP 707 A 1 HETATM 12 C C3' UDP . . . G 6 13.794 42.975 21.449 1 53.43 ? C3' UDP 707 A 1 HETATM 13 C C4' UDP . . . G 6 15.263 42.86 21.074 1 54.52 ? C4' UDP 707 A 1 HETATM 14 O O4' UDP . . . G 6 15.977 43.515 22.102 1 54.37 ? O4' UDP 707 A 1 HETATM 15 O O3' UDP . . . G 6 13.42 41.749 22.049 1 50.76 ? O3' UDP 707 A 1 HETATM 16 C C5' UDP . . . G 6 15.629 43.47 19.713 1 54.51 ? C5' UDP 707 A 1 HETATM 17 O O5' UDP . . . G 6 15.321 44.848 19.655 1 57.79 ? O5' UDP 707 A 1 HETATM 18 P PA UDP . . . G 6 14.173 45.393 18.659 1 57.56 ? PA UDP 707 A 1 HETATM 19 O O1A UDP . . . G 6 13.101 44.387 18.472 1 59.41 ? O1A UDP 707 A 1 HETATM 20 O O2A UDP . . . G 6 13.658 46.681 19.177 1 55.72 ? O2A UDP 707 A 1 HETATM 21 O O3A UDP . . . G 6 14.962 45.559 17.28 1 56.55 ? O3A UDP 707 A 1 HETATM 22 P PB UDP . . . G 6 14.286 45.347 15.84 1 52.67 ? PB UDP 707 A 1 HETATM 23 O O1B UDP . . . G 6 15.318 45.831 14.889 1 53.89 ? O1B UDP 707 A 1 HETATM 24 O O2B UDP . . . G 6 13.048 46.138 15.695 1 55.85 ? O2B UDP 707 A 1 HETATM 25 O O3B UDP . . . G 6 13.923 43.926 15.591 1 56.24 ? O3B UDP 707 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 25 #